I can't think of a really good BE off the top of my head, but I can think of HEs that feel like BEs and left a strong impression. For example, Okita Souji's HE in Hakuoki: it's said that he and the heroine are resting on the grass, but it really gives off the feeling that he'll never wake up again. The Ara and Ki routes in Ken ga Kimi are the same—they're generally part of the Sword route rather than the Kimi route, so most of them are fairly tragic. Even if something looks like a good ending, in the FD it gets turned into a BE. Take Kuroba Saneyoshi's, for instance—maybe choosing the Sword fits his personality better? The Wa route's development is pretty good too. One of Suzukake's routes may look like a BE, but I actually think it's quite nice—it's another form of companionship XD I can't say more without spoiling.
There's something about getting a peaceful moment together while knowing it might not last that makes it hit harder. "Another form of companionship" has me curious too 
I can see how an ending could feel romantic even if it isn't a happy one, especially if it feels true to the characters.